7PF3

Nucleosome 4 of the 4x187 nucleosome array containing H1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory.

Dombrowski, M.Engeholm, M.Dienemann, C.Dodonova, S.Cramer, P.

(2022) Nat Struct Mol Biol 29: 493-501

  • DOI: https://doi.org/10.1038/s41594-022-00768-w
  • Primary Citation of Related Structures:  
    7PET, 7PEU, 7PEV, 7PEW, 7PEX, 7PEY, 7PEZ, 7PF0, 7PF2, 7PF3, 7PF4, 7PF5, 7PF6, 7PFA, 7PFC, 7PFD, 7PFE, 7PFF, 7PFT, 7PFU, 7PFV, 7PFW, 7PFX

  • PubMed Abstract: 

    Throughout the genome, nucleosomes often form regular arrays that differ in nucleosome repeat length (NRL), occupancy of linker histone H1 and transcriptional activity. Here, we report cryo-EM structures of human H1-containing tetranucleosome arrays with four physiologically relevant NRLs. The structures show a zig-zag arrangement of nucleosomes, with nucleosomes 1 and 3 forming a stack. H1 binding to stacked nucleosomes depends on the NRL, whereas H1 always binds to the non-stacked nucleosomes 2 and 4. Short NRLs lead to altered trajectories of linker DNA, and these altered trajectories sterically impair H1 binding to the stacked nucleosomes in our structures. As the NRL increases, linker DNA trajectories relax, enabling H1 contacts and binding. Our results provide an explanation for why arrays with short NRLs are depleted of H1 and suited for transcription, whereas arrays with long NRLs show full H1 occupancy and can form transcriptionally silent heterochromatin regions.


  • Organizational Affiliation

    Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2A [auth k],
E [auth o]
136Homo sapiensMutation(s): 1 
Gene Names: HIST2H3AHIST2H3CH3F2H3FMHIST2H3D
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Find proteins for Q71DI3 (Homo sapiens)
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PHAROS:  Q71DI3
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UniProt GroupQ71DI3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4B [auth l],
F [auth p]
103Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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PHAROS:  P62805
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UniProt GroupP62805
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/EC [auth m],
G [auth q]
147Homo sapiensMutation(s): 0 
Gene Names: H2AC4H2AFMHIST1H2ABH2AC8H2AFAHIST1H2AE
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Find proteins for P04908 (Homo sapiens)
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PHAROS:  P04908
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-KD [auth n],
H [auth r]
126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BKH2BFTHIRIP1
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Find proteins for O60814 (Homo sapiens)
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PHAROS:  O60814
GTEx:  ENSG00000197903 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H1.4K [auth s]218Homo sapiensMutation(s): 0 
Gene Names: H1-4H1F4HIST1H1E
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Find proteins for P10412 (Homo sapiens)
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PHAROS:  P10412
GTEx:  ENSG00000168298 
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (167-MER)I [auth J]167synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (167-MER)J [auth I]167synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union882357

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2024-07-17
    Changes: Data collection, Refinement description